Parallel classification and feature selection in microarray data using SPRINT

Mitchell, Lawrence; Sloan, Terence M.; Mewissen, Muriel; Ghazal, Peter; Forster, Thorsten; Piotrowski, Michal; Trew, Arthur

doi:10.1002/cpe.2928

Parallel classification and feature selection in microarray data using SPRINT

Mitchell, Lawrence; Sloan, Terence M.; Mewissen, Muriel; Ghazal, Peter; Forster, Thorsten; Piotrowski, Michal; Trew, Arthur

Authors

Lawrence Mitchell

Terence M. Sloan

Muriel Mewissen

Peter Ghazal

Thorsten Forster

Michal Piotrowski

Arthur Trew

Abstract

The statistical language R is favoured by many biostatisticians for processing microarray data. In recent times, the quantity of data that can be obtained in experiments has risen significantly, making previously fast analyses time consuming or even not possible at all with the existing software infrastructure. High performance computing (HPC) systems offer a solution to these problems but at the expense of increased complexity for the end user. The Simple Parallel R Interface is a library for R that aims to reduce the complexity of using HPC systems by providing biostatisticians with drop‐in parallelised replacements of existing R functions. In this paper we describe parallel implementations of two popular techniques: exploratory clustering analyses using the random forest classifier and feature selection through identification of differentially expressed genes using the rank product method.

Citation

Mitchell, L., Sloan, T. M., Mewissen, M., Ghazal, P., Forster, T., Piotrowski, M., & Trew, A. (2014). Parallel classification and feature selection in microarray data using SPRINT. Concurrency and Computation: Practice and Experience, 26(4), 854-865. https://doi.org/10.1002/cpe.2928

Journal Article Type	Article
Acceptance Date	Aug 21, 2012
Online Publication Date	Sep 13, 2012
Publication Date	Mar 25, 2014
Deposit Date	Aug 1, 2018
Publicly Available Date	Aug 2, 2018
Journal	Concurrency and Computation: Practice and Experience
Print ISSN	1532-0626
Electronic ISSN	1532-0634
Publisher	Wiley
Peer Reviewed	Peer Reviewed
Volume	26
Issue	4
Pages	854-865
DOI	https://doi.org/10.1002/cpe.2928
Related Public URLs	https://www.ncbi.nlm.nih.gov/pubmed/24883047

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Copyright Statement
This is the accepted version of the following article: Mitchell, Lawrence, Sloan, Terence M., Mewissen, Muriel, Ghazal, Peter, Forster, Thorsten, Piotrowski, Michal & Trew, Arthur (2014). Parallel classification and feature selection in microarray data using SPRINT. Concurrency and Computation: Practice and Experience 26(4): 854-865, which has been published in final form at https://doi.org/10.1002/cpe.2928. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.